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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ), 'gf_id' => 'HOM05D001145', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001145' ), 'data_identifier' => 'HOM05D001145', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001145', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p16910' => 'bna', 'A01p26740' => 'bna', 'A03p26990' => 'bna', 'Aa31LG4G14210' => 'aar', 'Aa31LG6G8060' => 'aar', 'Aa31LG6G8070' => 'aar', 'Aa31LG7G11580' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4031' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.4808' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2361' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3366' => 'aag', 'Actinidia06455' => 'ach', 'Actinidia22279' => 'ach', 'Actinidia24152' => 'ach', 'Ah.01g014130' => 'amhyb', 'Ah.04g149610' => 'amhyb', 'Ah.04g161530' => 'amhyb', 'Ah.06g190590' => 'amhyb', 'Ah.12g060390' => 'amhyb', 'AL4G15860' => 'aly', 'AL5G23340' => 'aly', 'AL7G27430' => 'aly', 'Aqoxy213s001' => 'aox', 'Aqoxy2G00543_Aqoxy2G00544' => 'aox', 'Aqoxy2G00545' => 'aox', 'Aqoxy2G00546' => 'aox', 'Aqoxy2G00547_Aqoxy2G00548' => 'aox', 'Aqoxy2G01627' => 'aox', 'Aqoxy7G03277' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KX6TS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4585DL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GG70IM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5NNU3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KD1GVP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VKSA8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZP8Y56' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSH2T8' => 'arhy', 'AT2G24820' => 'ath', 'AT3G44880' => 'ath', 'AT4G25650' => 'ath', 'ATR0043G010' => 'atr', 'ATR0043G038' => 'atr', 'ATR0580G386' => 'atr', 'ATR0737G111' => 'atr', 'Atru.BG.19.p' => 'acertr', 'Atru.chr2.672' => 'acertr', 'Atru.chr2.673' => 'acertr', 'Atru.chr2.675' => 'acertr', 'Atru.chr3.2069' => 'acertr', 'Atru.chr3.3503' => 'acertr', 'Atru.chr4.1730' => 'acertr', 'AUR62000005' => 'cqu', 'AUR62000006' => 'cqu', 'AUR62014978' => 'cqu', 'AUR62019174' => 'cqu', 'AUR62019175' => 'cqu', 'AUR62024771' => 'cqu', 'AUR62025751' => 'cqu', 'AUR62029149' => 'cqu', 'AUR62029155' => 'cqu', 'AUR62032447' => 'cqu', 'BcaB01g02999' => 'bca', 'BcaB01g03000' => 'bca', 'BcaB05g23052' => 'bca', 'BcaC09g49659' => 'bca', 'BolC1t02044H' => 'bol', 'BolC1t03382H' => 'bol', 'BolC3t15580H' => 'bol', 'BraA01t01643Z' => 'bra', 'BraA01t02603Z' => 'bra', 'BraA03t11910Z' => 'bra', 'C01p21190' => 'bna', 'C01p34130' => 'bna', 'C03p32390' => 'bna', 'CAN.G1563.12' => 'can', 'CAN.G1563.13' => 'can', 'CAN.G546.53' => 'can', 'CAN.G566.49' => 'can', 'CANSAT11G0354' => 'cansat', 'CANSAT11G1143' => 'cansat', 'CANSAT11G1678' => 'cansat', 'CANSAT11G1975' => 'cansat', 'CANSAT11G2536' => 'cansat', 'CANSAT25G1628' => 'cansat', 'CANSAT64G1016' => 'cansat', 'CARHR151160' => 'chi', 'CARHR233090' => 'chi', 'CARHR294570' => 'chi', 'Carub.0004s0444' => 'cru', 'Carub.0005s1062' => 'cru', 'Carub.0007s1532' => 'cru', 'Carub.0238s0002' => 'cru', 'Ca_15787_v3' => 'car', 'Ca_17945_v3' => 'car', 'Ca_19325_v3' => 'car', 'CBR_g19416' => 'cbr', 'CBR_g19419' => 'cbr', 'CBR_g19421' => 'cbr', 'CBR_g26035' => 'cbr', 'CBR_g3534' => 'cbr', 'CBR_g37742' => 'cbr', 'CBR_g49638' => 'cbr', 'CBR_g49646' => 'cbr', 'CBR_g49649' => 'cbr', 'CBR_g53748' => 'cbr', 'CBR_g81620' => 'cbr', 'Cc01_g00670' => 'ccan', 'Cc01_g00730' => 'ccan', 'Cc01_g10220' => 'ccan', 'Cc08_g06700' => 'ccan', 'CDE02G2320' => 'cde', 'CDE02G4623' => 'cde', 'CDE04G1965' => 'cde', 'CDE07G1511' => 'cde', 'Cfa009573' => 'cfa', 'Cfa009576' => 'cfa', 'Cfa010140' => 'cfa', 'Cfa010141' => 'cfa', 'Cfa010142' => 'cfa', 'Cfa013013' => 'cfa', 'Cfa021185' => 'cfa', 'Cfa021220' => 'cfa', 'Cfa021221' => 'cfa', 'Ciclev10007702m.g' => 'ccl', 'Ciclev10007965m.g' => 'ccl', 'Ciclev10014836m.g' => 'ccl', 'Ciclev10014840m.g' => 'ccl', 'Ciclev10028147m.g' => 'ccl', 'CiPaw.07G232800' => 'cil', 'CiPaw.08G004400' => 'cil', 'CiPaw.13G144900' => 'cil', 'CiPaw.14G107000' => 'cil', 'CiPaw.14G135400' => 'cil', 'CiPaw.14G135500' => 'cil', 'ClCG01G013870' => 'cla', 'ClCG03G014420' => 'cla', 'ClCG03G014430' => 'cla', 'ClCG03G014440' => 'cla', 'ClCG05G016090' => 'cla', 'COL.COLO4_00097' => 'col', 'COL.COLO4_18918' => 'col', 'COL.COLO4_18919' => 'col', 'COL.COLO4_18920' => 'col', 'COL.COLO4_18970' => 'col', 'COL.COLO4_19206' => 'col', 'COL.COLO4_35035' => 'col', 'COL.COLO4_35036' => 'col', 'COL.COLO4_35040' => 'col', 'Cpa.g.sc119.59' => 'cpa', 'Cpa.g.sc119.60' => 'cpa', 'Cpa.g.sc148.47' => 'cpa', 'Cpa.g.sc47.4' => 'cpa', 'Cre03.g173450' => 'cre', 'Cre06.g278245' => 'cre', 'Cre06.g305650' => 'cre', 'Cre10.g450550' => 'cre', 'Cre11.g476500' => 'cre', 'Cre13.g583050' => 'cre', 'Cre17.g724600' => 'cre', 'Cre17.g724700' => 'cre', 'CsaV3_1G014100' => 'csa', 'CsaV3_1G014120' => 'csa', 'CsaV3_1G041770' => 'csa', 'CsaV3_1G041780' => 'csa', 'CsaV3_1G041790' => 'csa', 'CsaV3_1G041800' => 'csa', 'CsaV3_1G041810' => 'csa', 'CsaV3_4G036370' => 'csa', 'CSS0007167' => 'camsi', 'CSS0018677' => 'camsi', 'CSS0024763' => 'camsi', 'CSS0032816' => 'camsi', 'CSS0034347' => 'camsi', 'CSS0043219' => 'camsi', 'DCAR_004584' => 'dca', 'DCAR_022680' => 'dca', 'DCAR_029866' => 'dca', 'DCAR_029867' => 'dca', 'Dinv16229' => 'din', 'Dinv16232' => 'din', 'Dinv16415' => 'din', 'Duzib150G0254' => 'dzi', 'Duzib150G0831' => 'dzi', 'Duzib168G0121' => 'dzi', 'Duzib187G1480' => 'dzi', 'ECA238G2447' => 'eca', 'ECA238G2560' => 'eca', 'ECA238G3129' => 'eca', 'ECA238G3460' => 'eca', 'ECA238G3584' => 'eca', 'ECA238G4704' => 'eca', 'ECA246G4066' => 'eca', 'ECA248G1672' => 'eca', 'EL10Ac2g02451' => 'bvu', 'EL10Ac2g02452' => 'bvu', 'EL10Ac4g10372' => 'bvu', 'EL10Ac9g22627' => 'bvu', 'Eucgr.B03924' => 'egr', 'Eucgr.C04031' => 'egr', 'Eucgr.J01727' => 'egr', 'Eucgr.J01820' => 'egr', 'Eucgr.J01823' => 'egr', 'FAN01G0736' => 'fan', 'FAN01G1212' => 'fan', 'FAN01G2243' => 'fan', 'FAN03G0986' => 'fan', 'FAN03G1826' => 'fan', 'FAN06G4677' => 'fan', 'FAN10G2913' => 'fan', 'FAN10G4042' => 'fan', 'FAN11G1509' => 'fan', 'FAN11G3213' => 'fan', 'FAN15G1263' => 'fan', 'FAN16G0444' => 'fan', 'FAN21G1808' => 'fan', 'FAN21G3468' => 'fan', 'FAN25G1127' => 'fan', 'FAN25G3342' => 'fan', 'FAN27G3317' => 'fan', 'FvH4_2g41330' => 'fve', 'FvH4_3g30560' => 'fve', 'FvH4_3g45360' => 'fve', 'FvH4_3g45400' => 'fve', 'FvH4_3g45401' => 'fve', 'FvH4_7g02720' => 'fve', 'FvH4_7g02730' => 'fve', 'FvH4_7g02731' => 'fve', 'Glyma.04G059800' => 'gma', 'Glyma.05G156300' => 'gma', 'Glyma.06G060200' => 'gma', 'Glyma.08G114400' => 'gma', 'Glyma.11G192300' => 'gma', 'Glyma.12G082100' => 'gma', 'Glyma.17G221500' => 'gma', 'Gohir.A05G060800' => 'ghi', 'Gohir.A07G105000' => 'ghi', 'Gohir.A08G010950' => 'ghi', 'Gohir.A08G011000' => 'ghi', 'Gohir.A08G011100' => 'ghi', 'Gohir.D05G063000' => 'ghi', 'Gohir.D07G109100' => 'ghi', 'Gohir.D08G021250' => 'ghi', 'Gohir.D08G021300' => 'ghi', 'Gohir.D08G021400' => 'ghi', 'Gohir.D08G021500' => 'ghi', 'Gorai.001G117200' => 'gra', 'Gorai.004G016200' => 'gra', 'Gorai.004G016300' => 'gra', 'Gorai.004G016400' => 'gra', 'Gorai.009G064000' => 'gra', 'GSVIVG01025437001' => 'vvi', 'GSVIVG01025438001' => 'vvi', 'GSVIVG01025441001' => 'vvi', 'GSVIVG01025444001' => 'vvi', 'GSVIVG01025446001' => 'vvi', 'GSVIVG01031457001' => 'vvi', 'GSVIVG01036007001' => 'vvi', 'HanXRQChr03g0090341' => 'han', 'HanXRQChr03g0090371' => 'han', 'HanXRQChr06g0179321' => 'han', 'HanXRQChr06g0179331' => 'han', 'HanXRQChr10g0278441' => 'han', 'HanXRQChr10g0278451' => 'han', 'HanXRQChr11g0346011' => 'han', 'HanXRQChr14g0434611' => 'han', 'HanXRQChr14g0434621' => 'han', 'HanXRQChr14g0435001' => 'han', 'HanXRQChr14g0435011' => 'han', 'HanXRQChr14g0435021' => 'han', 'HanXRQChr14g0435031' => 'han', 'HanXRQChr14g0435201' => 'han', 'HanXRQChr14g0435211' => 'han', 'HanXRQChr14g0435231' => 'han', 'HanXRQChr14g0435281' => 'han', 'HanXRQChr14g0435291' => 'han', 'HanXRQChr14g0435311' => 'han', 'HanXRQChr14g0435321' => 'han', 'HanXRQChr14g0436431' => 'han', 'HanXRQChr14g0436441' => 'han', 'HanXRQChr14g0437751' => 'han', 'HanXRQChr14g0437761' => 'han', 'HanXRQChr14g0437771' => 'han', 'HanXRQChr14g0437781' => 'han', 'HanXRQChr14g0437811' => 'han', 'HanXRQChr14g0437821' => 'han', 'HanXRQChr14g0437831' => 'han', 'HanXRQChr14g0458101' => 'han', 'HanXRQChr17g0536341' => 'han', 'Haze_11468' => 'cav', 'Haze_23528' => 'cav', 'Haze_23533' => 'cav', 'Hma1.2p1_0392F.1_g142980' => 'hma', 'Hma1.2p1_0772F.1_g215990' => 'hma', 'Hma1.2p1_0772F.1_g216000' => 'hma', 'Hma1.2p1_0843F.1_g227360' => 'hma', 'HPP92_008396' => 'vpl', 'HPP92_017165' => 'vpl', 'HPP92_017541' => 'vpl', 'HPP92_017542' => 'vpl', 'Hund02973' => 'sun', 'Hund07585' => 'sun', 'Hund07587' => 'sun', 'Hund07589' => 'sun', 'Lalb_Chr01g0004621' => 'lal', 'Lalb_Chr08g0244481' => 'lal', 'Lalb_Chr13g0295041' => 'lal', 'Lj1A530G29' => 'lonja', 'Lj1C213G3' => 'lonja', 'Lj1C538G6' => 'lonja', 'Lj1g0021239' => 'lja', 'Lj2A1005T32' => 'lonja', 'Lj2A729T35' => 'lonja', 'Lj2C729G11' => 'lonja', 'Lj2C729T4' => 'lonja', 'Lj3g0004371' => 'lja', 'Lj4g0005676' => 'lja', 'Lj4g0015134' => 'lja', 'Lj6g0004877' => 'lja', 'Lj6g0015066' => 'lja', 'Lj7A738T100' => 'lonja', 'Lsat_1_v5_gn_1_64861' => 'lsa', 'Lsat_1_v5_gn_1_64901' => 'lsa', 'Lsat_1_v5_gn_2_52580' => 'lsa', 'Lsat_1_v5_gn_3_22540' => 'lsa', 'Manes.04G012500' => 'mes', 'Manes.15G107301' => 'mes', 'Manes.15G107401' => 'mes', 'Manes.15G107500' => 'mes', 'Manes.15G107600' => 'mes', 'Manes.15G107700' => 'mes', 'Manes.16G132300' => 'mes', 'Mapoly0028s0113' => 'mpo', 'Mapoly0030s0036' => 'mpo', 'Mapoly0030s0137' => 'mpo', 'Mapoly0037s0111' => 'mpo', 'Mapoly0046s0012' => 'mpo', 'Mapoly0047s0026' => 'mpo', 'MBI04_g09724_MAGBIO' => 'mbi', 'MBI15_g07484_MAGBIO' => 'mbi', 'MCO11G354' => 'mco', 'MCO15G515' => 'mco', 'MCO16G103' => 'mco', 'MD03G1005500' => 'mdo', 'MD08G1051400' => 'mdo', 'MD08G1051600' => 'mdo', 'MD11G1008100' => 'mdo', 'MD11G1008200' => 'mdo', 'MD11G1149200' => 'mdo', 'Medtr3g105820' => 'mtr', 'Medtr4g057200' => 'mtr', 'Medtr8g085790' => 'mtr', 'Medtr8g085810' => 'mtr', 'Medtr8g085820' => 'mtr', 'Medtr8g085840' => 'mtr', 'MELO3C004867.2' => 'cme', 'MELO3C015590.2' => 'cme', 'MELO3C015592.2' => 'cme', 'MELO3C015593.2' => 'cme', 'MELO3C015595.2' => 'cme', 'MELO3C016944.2' => 'cme', 'MELO3C029304.2' => 'cme', 'MELO3C035541.2' => 'cme', 'MELO3C035546.2' => 'cme', 'Migut.A00391' => 'egut', 'Migut.D02297' => 'egut', 'Migut.D02539' => 'egut', 'Migut.D02549' => 'egut', 'MSTRG.21084' => 'ama', 'Nitab4.5_0000173g0160' => 'nta', 'Nitab4.5_0000668g0080' => 'nta', 'Nitab4.5_0001110g0090' => 'nta', 'Nitab4.5_0002162g0210' => 'nta', 'Nitab4.5_0003134g0120' => 'nta', 'Nitab4.5_0009628g0010' => 'nta', 'Nn2g12480' => 'nnu', 'Nn2g13867' => 'nnu', 'Oeu007728.1' => 'oeu', 'Oeu034670.1' => 'oeu', 'Oeu048541.1' => 'oeu', 'Oeu059668.1' => 'oeu', 'Oeu059670.1' => 'oeu', 'Os02g0792800' => 'osa', 'Os03g0146400' => 'osa', 'Os03g0805600' => 'osa', 'Os03g0805700' => 'osa', 'Os03g0805900' => 'osa', 'Os03g0806300' => 'osa', 'Peaxi162Scf00459g00119' => 'pax', 'Peaxi162Scf00502g00713' => 'pax', 'Peaxi162Scf00502g00714' => 'pax', 'Peaxi162Scf00983g00004' => 'pax', 'PGR044G1085' => 'pgr', 'PGR102G3025' => 'pgr', 'PGR119G0075' => 'pgr', 'PGSC0003DMG400000457' => 'stu', 'PGSC0003DMG400002967' => 'stu', 'PGSC0003DMG400010641' => 'stu', 'PGSC0003DMG401029274' => 'stu', 'Phvul.002G236600' => 'pvu', 'Phvul.002G236700' => 'pvu', 'Phvul.009G086000' => 'pvu', 'Phvul.011G086700' => 'pvu', 'Potri.001G005700' => 'ptr', 'Potri.001G005900' => 'ptr', 'Potri.003G218900' => 'ptr', 'Potri.003G219000' => 'ptr', 'Potri.003G219400' => 'ptr', 'Potri.003G219550' => 'ptr', 'Potri.004G217200' => 'ptr', 'Potri.006G267300' => 'ptr', 'Potri.009G004100' => 'ptr', 'Potri.018G015700' => 'ptr', 'Pp3c11_12710' => 'ppa', 'Pp3c1_12190' => 'ppa', 'Pp3c1_12270' => 'ppa', 'Pp3c1_40790' => 'ppa', 'Pp3c2_6220' => 'ppa', 'Pp3c3_19130' => 'ppa', 'Pp3c7_15550' => 'ppa', 'PRCOL_00001036' => 'pco', 'PRCOL_00006127' => 'pco', 'PRCOL_00006185' => 'pco', 'Prupe.1G397100' => 'ppe', 'Prupe.1G397200' => 'ppe', 'Prupe.6G005300' => 'ppe', 'Prupe.6G113600' => 'ppe', 'Psat5g033120' => 'psa', 'Psat7g072080' => 'psa', 'Psat7g223720' => 'psa', 'PSO063G6900' => 'pso', 'PSO339G1579' => 'pso', 'PSO339G1934' => 'pso', 'PSO384G3103' => 'pso', 'PSO782G5236' => 'pso', 'PSO801G0093' => 'pso', 'QL01p008547' => 'qlo', 'QL01p008558' => 'qlo', 'QL01p008572' => 'qlo', 'QL01p008654' => 'qlo', 'QL01p008665' => 'qlo', 'QL01p014896' => 'qlo', 'QL02p018077' => 'qlo', 'RcHm_v2.0_Chr1g0321981' => 'rch', 'RcHm_v2.0_Chr5g0056561' => 'rch', 'RcHm_v2.0_Chr5g0083181' => 'rch', 'RcHm_v2.0_Chr5g0083211' => 'rch', 'RcHm_v2.0_Chr6g0299151' => 'rch', 'Rhsim01G0184700' => 'rsi', 'Rhsim01G0184800' => 'rsi', 'Rhsim02G0217800' => 'rsi', 'Rhsim02G0217900' => 'rsi', 'Rhsim13G0101100' => 'rsi', 'Sabra01G0004100' => 'sbr', 'Sabra01G0004200' => 'sbr', 'Sabra01G0004300' => 'sbr', 'Sabra03G0163300' => 'sbr', 'Sabra03G0163400' => 'sbr', 'Sabra04G0147900' => 'sbr', 'Sabra06G0209600' => 'sbr', 'Sabra09G0001800' => 'sbr', 'Sabra18G0019000' => 'sbr', 'SalBow2G0280' => 'sbo', 'SalBow2G0307' => 'sbo', 'SalBow2G1502' => 'sbo', 'SalBow2G2527' => 'sbo', 'SalBow4G1746' => 'sbo', 'SalBow6G5394' => 'sbo', 'Sc06g0000310' => 'sci', 'Sc06g0000320' => 'sci', 'Sc16g0012170' => 'sci', 'Sc21g0000340' => 'sci', 'Sed0005522' => 'sed', 'Sed0018344' => 'sed', 'Sed0024158' => 'sed', 'Sed0027737' => 'sed', 'SEGI_07370' => 'sgi', 'SEGI_08762' => 'sgi', 'SEGI_17342' => 'sgi', 'SEGI_25545' => 'sgi', 'SEGI_32230' => 'sgi', 'SGA_v2.0_scaffold27G11573' => 'sas', 'SGA_v2.0_scaffold27G11633' => 'sas', 'SGA_v2.0_scaffold6G03402' => 'sas', 'SMO139G0147' => 'smo', 'SMO348G0071' => 'smo', 'Solyc04g039870.3' => 'sly', 'Solyc04g039880.3' => 'sly', 'Solyc04g039890.1' => 'sly', 'Solyc04g040160.4' => 'sly', 'Solyc11g066440.2' => 'sly', 'Solyc12g096550.2' => 'sly', 'Sopen04g009970' => 'spe', 'Sopen11g026190' => 'spe', 'Sopen12g032380' => 'spe', 'Sp4g03840' => 'spa', 'Sp5g16340' => 'spa', 'Sp7g23690' => 'spa', 'TAR626G1257' => 'tar', 'TAR633G2303' => 'tar', 'TAR633G2395' => 'tar', 'TAR633G2538' => 'tar', 'TAR633G2596' => 'tar', 'THA.LOC104799047' => 'tha', 'THA.LOC104803608' => 'tha', 'THA.LOC104810883' => 'tha', 'THA.LOC104811071' => 'tha', 'Thecc.09G013700' => 'tca', 'Thecc.09G208200' => 'tca', 'Thecc.09G298000' => 'tca', 'Thhalv10000113m.g' => 'esa', 'Thhalv10002475m.g' => 'esa', 'Thhalv10024869m.g' => 'esa', 'TPR.G1896' => 'tpr', 'TPR.G24382' => 'tpr', 'TPR.G34406' => 'tpr', 'TPR.G36804' => 'tpr', 'TWI32G0797' => 'twi', 'TWI32G1219' => 'twi', 'TWI34G0371' => 'twi', 'TWI60G0221' => 'twi', 'TWI60G0780' => 'twi', 'TWI60G1063' => 'twi', 'TWI75G1305' => 'twi', 'unitig_0.g1496' => 'ugi', 'unitig_22.g5859' => 'ugi', 'unitig_747.g21970' => 'ugi', 'vmacro03252' => 'vma', 'vmacro11276' => 'vma', 'vmacro12605' => 'vma', 'VMungo0251G0475' => 'vmu', 'VMungo1127G2205' => 'vmu', 'VMungo1309G0760' => 'vmu', 'Zm00001eb003760' => 'zma', 'Zm00001eb061510' => 'zma', 'Zm00001eb073210' => 'zma', 'Zm00001eb073220' => 'zma', 'Zm00001eb081040' => 'zma', 'Zm00001eb081050' => 'zma', 'Zm00001eb257630' => 'zma', 'Zm00001eb260500' => 'zma', 'Zm00001eb359770' => 'zma' ) $gf_id = 'HOM05D001145' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001145' ) $data_identifier = 'HOM05D001145' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 4, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 7, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 10, 'bca' => (int) 4, 'bol' => (int) 3, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 11, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 9, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 9, 'cpa' => (int) 4, 'cre' => (int) 8, 'csa' => (int) 8, 'camsi' => (int) 6, 'dca' => (int) 4, 'din' => (int) 3, 'dzi' => (int) 4, 'eca' => (int) 8, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 17, 'fve' => (int) 8, 'gma' => (int) 7, 'ghi' => (int) 11, 'gra' => (int) 5, 'vvi' => (int) 7, 'han' => (int) 31, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 3, 'lonja' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 7, 'mpo' => (int) 6, 'mbi' => (int) 2, 'mco' => (int) 3, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 9, 'egut' => (int) 4, 'ama' => (int) 1, 'nta' => (int) 6, 'nnu' => (int) 2, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 10, 'ppa' => (int) 7, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 9, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359770' $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